I can imagine that some very advanced alien civilisations might adopt a low profile for reasons other than fear. Perhaps they prefer to blend into the background out of politeness; they might prefer the appearance of a galaxy which looks as if it is uninhabited.
They might even hide in this way for our benefit, so that we can continue to behave as if they did not exist, which for all intents and purposes they don't.
This leads on naturally to the Zoo hypothesis; we don't see them because we are being kept as specially preserved examples of our kind
http://en.wikipedia.org/wiki/Zoo_hypothesis
An ideal zoo might provide an environment in which the zookeepers were entirely invisible.
What does the Great Filter hypothesis tell us about such a situation? Well; there would obviously be a barrier for us to pass to move from the status of zoo exhibits to that of zookeepers. It may be the case that we would not be allowed to ever make that transition. We would remain as exhibits forever - and a filter which could potentially prevent us from passing to a higher status in the Galaxy would exist.